A hub-and-spoke, IOF-anchored application ontology for mammalian cell bioprocessing and RNA-seq data curation.
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Pre-requisites:
- Conda/Miniconda (for environment management)
make conda-env
conda activate mcbo
make install
make demoSee the Installation Guide for detailed setup instructions.
MCBO supports 8 competency questions.
See the full CQ documentation.
Answer competency questions using natural language with an LLM-powered agent:
# Install agent dependencies
make install-agent
# Set your API key
export OPENAI_API_KEY=sk-... # or ANTHROPIC_API_KEY
# Ask questions!
mcbo-agent-eval --data-dir data.sample --cq CQ1
mcbo-agent-eval --data-dir data.sample \
--cq "What genes are differentially expressed under Fed-batch vs Perfusion?"
# Or use local LLM (free, private)
make install-ollama
mcbo-agent-eval --data-dir data.sample --cq CQ1 --provider ollama📖 Agent Documentation - Full setup, customization, and MCP server integration.
| Section | Description |
|---|---|
| Installation | Environment setup and dependencies |
| Quick Start | Run the demo in minutes |
| Workflows | Data ingestion scenarios |
| CLI Reference | Command-line tools and CSV columns |
| Ontology Design | Modeling patterns and architecture |
| API Reference | Python package documentation |
| Development | Contributing and QC checks |
MIT License - see LICENSE for details.
MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology
Kimberly Robasky, James Morrissey, Markus Riedl, Andreas Dräger, Nicole Borth, Michael J Betenbaugh, Nathan E Lewis
bioRxiv 2026.01.05.697007; doi: https://doi.org/10.64898/2026.01.05.697007
This article is a preprint and has not been certified by peer review.
Supersedes: Robasky, K., Morrissey, J., Riedl, M., Dräger, A., Borth, N., Betenbaugh, M. J., & Lewis, N. E. (2025). MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology. ICBO-EAST 2025.